Myelodysplastic syndrome (MDS) has been long recognized as a collection of diseases characterized by ineffective hematopoiesis associated with impairment of differentiation and intra-medullary apoptosis. Moreover, patients with MDS often progress to acute myeloid leukemia (AML). The pathogenesis of MDS remains obscure, and effective therapies are lacking. One challenge is that MDS represents a diverse collection of diseases, categorized by often vague clinical criteria. One exception to this, however, is the 5q syndrome, which has distinct clinical characteristics and is associated with deletions of the long arm of chromosome 5. The disease gene for this syndrome has yet to be identified. We therefore propose here an ambitious genomics-based approach to the cloning of the 5q- syndrome disease gene, and to the discovery of small molecules that circumvent the differentiation block that is characteristic of MDS. In Aim 1, we will perform a systematic, RNA interference-based functional genomic screen in CD34+ primary hematopoietic progenitor cells to identify those genes in the critically deleted region of 5q that recapitulate the differentiation defect characteristic of MDS. In addition, we will perform fine-mapping of the 5q region using high density custom microarray comparative genomic hybridization (CGH) in order to identify patients with previously unrecognized, small deletions. Furthermore, we will utilize .a novel single-molecule sequencing method to resequence the candidate genes on 5q for mutations. In Aim 2, we will perform a high throughput gene expression-based small molecule screen using the GE-HTS method developed in our laboratory. Using this approach, we expect to identify small molecules (or drugs) capable of promoting the expansion and differentiation of hematopoietic progenitors. Such compounds would be valuable both as tool compounds with which to dissect the biology of MDS, and as potential starting points for the development of new therapies of MDS.